X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=a2d0559ad32291b7c97191f8b912d4ec1338d37d;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=22101487a711fb87e6d202a02bde3503cf92fac0;hpb=30b6afb62b0741f2ac9224a50929d2dd9ece1754;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 2210148..a2d0559 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -20,18 +20,16 @@ */ package jalview.gui; -import jalview.analysis.AlignmentSorter; +import jalview.api.FeatureSettingsControllerI; import jalview.bin.Cache; -import jalview.commands.OrderCommand; -import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.gui.Help.HelpId; import jalview.io.JalviewFileChooser; import jalview.schemes.AnnotationColourGradient; import jalview.schemes.GraduatedColor; import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; import jalview.ws.dbsources.das.api.jalviewSourceI; import java.awt.BorderLayout; @@ -56,10 +54,10 @@ import java.io.FileOutputStream; import java.io.InputStreamReader; import java.io.OutputStreamWriter; import java.io.PrintWriter; -import java.util.ArrayList; import java.util.Hashtable; import java.util.Iterator; import java.util.List; +import java.util.Set; import java.util.Vector; import javax.help.HelpSetException; @@ -91,7 +89,8 @@ import javax.swing.table.AbstractTableModel; import javax.swing.table.TableCellEditor; import javax.swing.table.TableCellRenderer; -public class FeatureSettings extends JPanel +public class FeatureSettings extends JPanel implements + FeatureSettingsControllerI { DasSourceBrowser dassourceBrowser; @@ -107,6 +106,8 @@ public class FeatureSettings extends JPanel Object[][] originalData; + private float originalTransparency; + final JInternalFrame frame; JScrollPane scrollPane = new JScrollPane(); @@ -123,8 +124,9 @@ public class FeatureSettings extends JPanel { this.af = af; fr = af.getFeatureRenderer(); - - transparency.setMaximum(100 - (int) (fr.transparency * 100)); + // allow transparency to be recovered + transparency.setMaximum(100 - (int) ((originalTransparency = fr + .getTransparency()) * 100)); try { @@ -134,15 +136,18 @@ public class FeatureSettings extends JPanel ex.printStackTrace(); } - table = new JTable() { + table = new JTable() + { @Override - public String getToolTipText(MouseEvent e) { - if (table.columnAtPoint(e.getPoint()) == 0) { + public String getToolTipText(MouseEvent e) + { + if (table.columnAtPoint(e.getPoint()) == 0) + { /* * Tooltip for feature name only */ - return JvSwingUtils.wrapTooltip(true, - MessageManager.getString("label.feature_settings_click_drag")); + return JvSwingUtils.wrapTooltip(true, MessageManager + .getString("label.feature_settings_click_drag")); } return null; } @@ -165,8 +170,8 @@ public class FeatureSettings extends JPanel if (SwingUtilities.isRightMouseButton(evt)) { popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0), - table.getValueAt(selectedRow, 1), fr.minmax, evt.getX(), - evt.getY()); + table.getValueAt(selectedRow, 1), fr.getMinMax(), + evt.getX(), evt.getY()); } else if (evt.getClickCount() == 2) { @@ -185,8 +190,8 @@ public class FeatureSettings extends JPanel if (evt.isPopupTrigger()) { popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0), - table.getValueAt(selectedRow, 1), fr.minmax, evt.getX(), - evt.getY()); + table.getValueAt(selectedRow, 1), fr.getMinMax(), + evt.getX(), evt.getY()); } } }); @@ -215,20 +220,19 @@ public class FeatureSettings extends JPanel } } }); -// table.setToolTipText(JvSwingUtils.wrapTooltip(true, -// MessageManager.getString("label.feature_settings_click_drag"))); + // table.setToolTipText(JvSwingUtils.wrapTooltip(true, + // MessageManager.getString("label.feature_settings_click_drag"))); scrollPane.setViewportView(table); dassourceBrowser = new DasSourceBrowser(this); dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER); - if (af.getViewport().featuresDisplayed == null - || fr.renderOrder == null) + if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder()) { fr.findAllFeatures(true); // display everything! } - setTableData(); + discoverAllFeatureData(); final PropertyChangeListener change; final FeatureSettings fs = this; fr.addPropertyChangeListener(change = new PropertyChangeListener() @@ -277,8 +281,7 @@ public class FeatureSettings extends JPanel final Object typeCol, final Hashtable minmax, int x, int y) { JPopupMenu men = new JPopupMenu(MessageManager.formatMessage( - "label.settings_for_param", new String[] - { type })); + "label.settings_for_param", new String[] { type })); JMenuItem scr = new JMenuItem( MessageManager.getString("label.sort_by_score")); men.add(scr); @@ -288,8 +291,7 @@ public class FeatureSettings extends JPanel public void actionPerformed(ActionEvent e) { - me.sortByScore(new String[] - { type }); + me.af.avc.sortAlignmentByFeatureScore(new String[] { type }); } }); @@ -300,8 +302,7 @@ public class FeatureSettings extends JPanel public void actionPerformed(ActionEvent e) { - me.sortByDens(new String[] - { type }); + me.af.avc.sortAlignmentByFeatureDensity(new String[] { type }); } }); @@ -422,27 +423,22 @@ public class FeatureSettings extends JPanel */ Hashtable typeWidth = null; - synchronized public void setTableData() + @Override + synchronized public void discoverAllFeatureData() { - if (fr.featureGroups == null) - { - fr.featureGroups = new Hashtable(); - } Vector allFeatures = new Vector(); Vector allGroups = new Vector(); SequenceFeature[] tmpfeatures; String group; for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++) { - if (af.getViewport().getAlignment().getSequenceAt(i) - .getDatasetSequence().getSequenceFeatures() == null) + tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i) + .getSequenceFeatures(); + if (tmpfeatures == null) { continue; } - tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i) - .getDatasetSequence().getSequenceFeatures(); - int index = 0; while (index < tmpfeatures.length) { @@ -458,10 +454,7 @@ public class FeatureSettings extends JPanel if (!allGroups.contains(group)) { allGroups.addElement(group); - if (group != null) - { - checkGroupState(group); - } + checkGroupState(group); } } @@ -479,21 +472,14 @@ public class FeatureSettings extends JPanel } /** + * Synchronise gui group list and check visibility of group * * @param group - * @return true if group has been seen before and is already added to set. + * @return true if group is visible */ private boolean checkGroupState(String group) { - boolean visible; - if (fr.featureGroups.containsKey(group)) - { - visible = ((Boolean) fr.featureGroups.get(group)).booleanValue(); - } - else - { - visible = true; // new group is always made visible - } + boolean visible = fr.checkGroupVisibility(group, true); if (groupPanel == null) { @@ -514,10 +500,8 @@ public class FeatureSettings extends JPanel if (alreadyAdded) { - return true; + return visible; } - - fr.featureGroups.put(group, new Boolean(visible)); final String grp = group; final JCheckBox check = new JCheckBox(group, visible); check.setFont(new Font("Serif", Font.BOLD, 12)); @@ -525,20 +509,18 @@ public class FeatureSettings extends JPanel { public void itemStateChanged(ItemEvent evt) { - fr.featureGroups.put(check.getText(), - new Boolean(check.isSelected())); - af.alignPanel.seqPanel.seqCanvas.repaint(); + fr.setGroupVisibility(check.getText(), check.isSelected()); + af.alignPanel.getSeqPanel().seqCanvas.repaint(); if (af.alignPanel.overviewPanel != null) { af.alignPanel.overviewPanel.updateOverviewImage(); } - resetTable(new String[] - { grp }); + resetTable(new String[] { grp }); } }); groupPanel.add(check); - return false; + return visible; } boolean resettingTable = false; @@ -565,7 +547,7 @@ public class FeatureSettings extends JPanel { tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i) - .getDatasetSequence().getSequenceFeatures(); + .getSequenceFeatures(); if (tmpfeatures == null) { continue; @@ -582,13 +564,8 @@ public class FeatureSettings extends JPanel continue; } - if (group == null || fr.featureGroups.get(group) == null - || ((Boolean) fr.featureGroups.get(group)).booleanValue()) + if (group == null || checkGroupState(group)) { - if (group != null) - { - checkGroupState(group); - } type = tmpfeatures[index].getType(); if (!visibleChecks.contains(type)) { @@ -623,19 +600,20 @@ public class FeatureSettings extends JPanel Object[][] data = new Object[fSize][3]; int dataIndex = 0; - if (fr.renderOrder != null) + if (fr.hasRenderOrder()) { if (!handlingUpdate) - { + { fr.findAllFeatures(groupChanged != null); // prod to update + // colourschemes. but don't + // affect display + // First add the checks in the previous render order, + // in case the window has been closed and reopened } - // colourschemes. but don't - // affect display - // First add the checks in the previous render order, - // in case the window has been closed and reopened - for (int ro = fr.renderOrder.length - 1; ro > -1; ro--) + List frl = fr.getRenderOrder(); + for (int ro = frl.size() - 1; ro > -1; ro--) { - type = fr.renderOrder[ro]; + type = frl.get(ro); if (!visibleChecks.contains(type)) { @@ -644,8 +622,8 @@ public class FeatureSettings extends JPanel data[dataIndex][0] = type; data[dataIndex][1] = fr.getFeatureStyle(type); - data[dataIndex][2] = new Boolean( - af.getViewport().featuresDisplayed.containsKey(type)); + data[dataIndex][2] = new Boolean(af.getViewport() + .getFeaturesDisplayed().isVisible(type)); dataIndex++; visibleChecks.removeElement(type); } @@ -663,7 +641,7 @@ public class FeatureSettings extends JPanel if (data[dataIndex][1] == null) { // "Colour has been updated in another view!!" - fr.renderOrder = null; + fr.clearRenderOrder(); return; } @@ -685,8 +663,8 @@ public class FeatureSettings extends JPanel if (groupPanel != null) { - groupPanel.setLayout(new GridLayout(fr.featureGroups.size() / 4 + 1, - 4)); + groupPanel.setLayout(new GridLayout( + fr.getFeatureGroupsSize() / 4 + 1, 4)); groupPanel.validate(); bigPanel.add(groupPanel, BorderLayout.NORTH); @@ -726,11 +704,13 @@ public class FeatureSettings extends JPanel void load() { JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] - { "fc" }, new String[] - { "Sequence Feature Colours" }, "Sequence Feature Colours"); + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), + new String[] { "fc" }, + new String[] { "Sequence Feature Colours" }, + "Sequence Feature Colours"); chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle(MessageManager.getString("label.load_feature_colours")); + chooser.setDialogTitle(MessageManager + .getString("label.load_feature_colours")); chooser.setToolTipText(MessageManager.getString("action.load")); int value = chooser.showOpenDialog(this); @@ -745,8 +725,7 @@ public class FeatureSettings extends JPanel file), "UTF-8"); jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours(); - jucs = jucs - .unmarshal(in); + jucs = jucs.unmarshal(in); for (int i = jucs.getColourCount() - 1; i >= 0; i--) { @@ -824,11 +803,13 @@ public class FeatureSettings extends JPanel void save() { JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] - { "fc" }, new String[] - { "Sequence Feature Colours" }, "Sequence Feature Colours"); + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), + new String[] { "fc" }, + new String[] { "Sequence Feature Colours" }, + "Sequence Feature Colours"); chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle(MessageManager.getString("label.save_feature_colours")); + chooser.setDialogTitle(MessageManager + .getString("label.save_feature_colours")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -843,9 +824,10 @@ public class FeatureSettings extends JPanel PrintWriter out = new PrintWriter(new OutputStreamWriter( new FileOutputStream(choice), "UTF-8")); - Iterator e = fr.featureColours.keySet().iterator(); - float[] sortOrder = new float[fr.featureColours.size()]; - String[] sortTypes = new String[fr.featureColours.size()]; + Set fr_colours = fr.getAllFeatureColours(); + Iterator e = fr_colours.iterator(); + float[] sortOrder = new float[fr_colours.size()]; + String[] sortTypes = new String[fr_colours.size()]; int i = 0; while (e.hasNext()) { @@ -962,9 +944,9 @@ public class FeatureSettings extends JPanel } } if (sort) - { + { jalview.util.QuickSort.sort(width, data); - // update global priority order + // update global priority order } updateFeatureRenderer(data, false); @@ -1068,7 +1050,7 @@ public class FeatureSettings extends JPanel { public void actionPerformed(ActionEvent e) { - sortByScore(null); + af.avc.sortAlignmentByFeatureScore(null); } }); sortByDens.setFont(JvSwingUtils.getLabelFont()); @@ -1078,7 +1060,22 @@ public class FeatureSettings extends JPanel { public void actionPerformed(ActionEvent e) { - sortByDens(null); + af.avc.sortAlignmentByFeatureDensity(null); + } + }); + help.setFont(JvSwingUtils.getLabelFont()); + help.setText(MessageManager.getString("action.help")); + help.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + try + { + Help.showHelpWindow(HelpId.SequenceFeatureSettings); + } catch (HelpSetException e1) + { + e1.printStackTrace(); + } } }); help.setFont(JvSwingUtils.getLabelFont()); @@ -1102,6 +1099,7 @@ public class FeatureSettings extends JPanel { public void actionPerformed(ActionEvent e) { + fr.setTransparency(originalTransparency); updateFeatureRenderer(originalData); close(); } @@ -1173,8 +1171,10 @@ public class FeatureSettings extends JPanel } }); this.add(tabbedPane, java.awt.BorderLayout.CENTER); - tabbedPane.addTab(MessageManager.getString("label.feature_settings"), settingsPane); - tabbedPane.addTab(MessageManager.getString("label.das_settings"), dasSettingsPane); + tabbedPane.addTab(MessageManager.getString("label.feature_settings"), + settingsPane); + tabbedPane.addTab(MessageManager.getString("label.das_settings"), + dasSettingsPane); bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH); transbuttons.add(optimizeOrder); transbuttons.add(invert); @@ -1198,131 +1198,6 @@ public class FeatureSettings extends JPanel settingsPane.add(buttonPanel, java.awt.BorderLayout.SOUTH); } - protected void sortByDens(String[] typ) - { - sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY); - } - - protected void sortBy(String[] typ, String methodText, final String method) - { - if (typ == null) - { - typ = getDisplayedFeatureTypes(); - } - String gps[] = null; - gps = getDisplayedFeatureGroups(); - if (typ != null) - { - ArrayList types = new ArrayList(); - for (int i = 0; i < typ.length; i++) - { - if (typ[i] != null) - { - types.add(typ[i]); - } - typ = new String[types.size()]; - types.toArray(typ); - } - } - if (gps != null) - { - ArrayList grps = new ArrayList(); - - for (int i = 0; i < gps.length; i++) - { - if (gps[i] != null) - { - grps.add(gps[i]); - } - } - gps = new String[grps.size()]; - grps.toArray(gps); - } - AlignmentPanel alignPanel = af.alignPanel; - AlignmentI al = alignPanel.av.getAlignment(); - - int start, stop; - SequenceGroup sg = alignPanel.av.getSelectionGroup(); - if (sg != null) - { - start = sg.getStartRes(); - stop = sg.getEndRes(); - } - else - { - start = 0; - stop = al.getWidth(); - } - SequenceI[] oldOrder = al.getSequencesArray(); - AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method); - af.addHistoryItem(new OrderCommand(methodText, oldOrder, alignPanel.av - .getAlignment())); - alignPanel.paintAlignment(true); - - } - - protected void sortByScore(String[] typ) - { - sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE); - } - - private String[] getDisplayedFeatureTypes() - { - String[] typ = null; - if (fr != null) - { - synchronized (fr.renderOrder) - { - typ = new String[fr.renderOrder.length]; - System.arraycopy(fr.renderOrder, 0, typ, 0, typ.length); - for (int i = 0; i < typ.length; i++) - { - if (af.viewport.featuresDisplayed.get(typ[i]) == null) - { - typ[i] = null; - } - } - } - } - return typ; - } - - private String[] getDisplayedFeatureGroups() - { - String[] gps = null; - ArrayList _gps = new ArrayList(); - if (fr != null) - { - - if (fr.featureGroups != null) - { - Iterator en = fr.featureGroups.keySet().iterator(); - int g = 0; - boolean valid = false; - while (en.hasNext()) - { - String gp = (String) en.next(); - Boolean on = (Boolean) fr.featureGroups.get(gp); - if (on != null && on.booleanValue()) - { - valid = true; - _gps.add(gp); - } - } - if (!valid) - { - return null; - } - else - { - gps = new String[_gps.size()]; - _gps.toArray(gps); - } - } - } - return gps; - } - public void fetchDAS_actionPerformed(ActionEvent e) { fetchDAS.setEnabled(false); @@ -1344,7 +1219,7 @@ public class FeatureSettings extends JPanel { SequenceI[] dataset, seqs; int iSize; - AlignViewport vp = af.getViewport(); + AlignmentViewport vp = af.getViewport(); if (vp.getSelectionGroup() != null && vp.getSelectionGroup().getSize() > 0) { @@ -1493,8 +1368,10 @@ public class FeatureSettings extends JPanel this.data = data; } - private String[] columnNames = - { MessageManager.getString("label.feature_type"), MessageManager.getString("action.colour"), MessageManager.getString("label.display") }; + private String[] columnNames = { + MessageManager.getString("label.feature_type"), + MessageManager.getString("action.colour"), + MessageManager.getString("label.display") }; private Object[][] data;